1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "DistributionWriter.h"
#include <code/Mock/constants.h>
#include <code/Mock/common_functions.h>
#include <sstream>
#include <iostream>
using namespace std;
#ifdef CONFIG_ASSERT
#include <assert.h>
#endif
DistributionWriter::DistributionWriter(){
m_gotFile=false;
}
void DistributionWriter::setBase(const char*base){
m_base=base;
}
void DistributionWriter::setRank(Rank rank){
m_rank=rank;
}
void DistributionWriter::write(int directory,int file,int sequence,
map<CoverageDepth,LargeCount>*all,map<CoverageDepth,LargeCount>*uniquelyColored,map<CoverageDepth,LargeCount>*uniquelyColoredAndAssembled,
const char*directoryName,const char*fileName){
openFile();
m_output_Buffer<<"<entry><directory>";
m_output_Buffer<<directoryName<<"</directory><file>"<<fileName<<"</file><sequence>";
m_output_Buffer<<sequence<<"</sequence>"<<endl;
m_output_Buffer<<"<raw>"<<endl;
m_output_Buffer<<"#Coverage depth Frequency"<<endl;
for(map<CoverageDepth,LargeCount>::iterator i=all->begin();
i!=all->end();i++){
m_output_Buffer<<i->first<<" "<<i->second<<endl;
}
m_output_Buffer<<"</raw>"<<endl;
m_output_Buffer<<"<uniquelyColored>"<<endl;
m_output_Buffer<<"#Coverage depth Frequency"<<endl;
for(map<CoverageDepth,LargeCount>::iterator i=uniquelyColored->begin();
i!=uniquelyColored->end();i++){
m_output_Buffer<<i->first<<" "<<i->second<<endl;
}
m_output_Buffer<<"</uniquelyColored>"<<endl;
m_output_Buffer<<"<uniquelyColoredAndAssembled>"<<endl;
m_output_Buffer<<"#Coverage depth Frequency"<<endl;
for(map<CoverageDepth,LargeCount>::iterator i=uniquelyColoredAndAssembled->begin();
i!=uniquelyColoredAndAssembled->end();i++){
m_output_Buffer<<i->first<<" "<<i->second<<endl;
}
m_output_Buffer<<"</uniquelyColoredAndAssembled>"<<endl;
m_output_Buffer<<"</entry>"<<endl;
flushFileOperationBuffer(false,&m_output_Buffer,&m_output,CONFIG_FILE_IO_BUFFER_SIZE);
}
void DistributionWriter::close(){
if(m_gotFile){
m_output_Buffer<<"</root>"<<endl;
flushFileOperationBuffer(true,&m_output_Buffer,&m_output,CONFIG_FILE_IO_BUFFER_SIZE);
m_output.close();
m_gotFile=false;
cout<<"[IO] Rank "<<m_rank<<" performed "<<m_operations<<" input/output operations on the file system from DistributionWriter."<<endl;
}
}
void DistributionWriter::openFile(){
if(m_gotFile){
return;
}
m_operations=0;
ostringstream rawDistribution;
rawDistribution<<m_base<<"/"<<m_rank<<".Distributions.xml";
m_output.open(rawDistribution.str().c_str());
cout<<"Opened "<<rawDistribution.str()<<endl;
m_output_Buffer<<"<?xml version=\"1.0\" encoding=\"UTF-8\"?>"<<endl;
m_output_Buffer<<"<root>"<<endl;
m_gotFile=true;
}
|
